[Bioc-devel] xps build problem on veracruz2

cstrato cstrato at aon.at
Fri Mar 24 19:37:09 CET 2017 


On 03/24/17 19:23, Hervé Pagès wrote:
> On 03/24/2017 11:10 AM, cstrato wrote:
>>
>>
>> On 03/24/17 18:02, Hervé Pagès wrote:
>>> On 03/24/2017 06:52 AM, cstrato wrote:
>>>> R/Bioc is still building on Mavericks,
>>>
>>> Not for R devel (3.4). The R folks have switched to El Capitan a few
>>> days ago:
>>>
>>
>> You are right, I did not check R devel.
>>
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs&s=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA&e=
>>>
>>>
>>>> and before was built on Snow
>>>> Leopard (which many people are sill using).
>>>>
>>>> Personally I think that it does not make much difference whether
>>>> Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.
>>>
>>> How much experience you have with setting a Mavericks or El Capitan
>>> build machine to build and distribute thousands of package binaries for
>>> hundreds ot thousands of users?
>>>
>>
>> You probably misunderstood what I wanted to say.
>>
>> It is clear to me that you are doing a great job distributing thousands
>> of package binaries. No one does know it better than me with the special
>> problems you have to build binaries for xps. I really appreciate that
>> during all these years you and Dan (and others) managed to support xps
>> like all other BioC packages.
>>
>> I meant that from the user standpoint it probably does not matter much
>> which of these three systems are used to build BioC, in contrast to
>> Sierra.
>
> Of course it matters. If you use an older OS than the one we use to
> produce the binaries then some binaries won't work for you. You keep
> missing the whole point.
>
> H.
>

Sorry, but I do understand this point. Users who are still using e.g. 
Snow Leopard (because they think this was the best system) will have 
problems. For that reason I thought that maybe it is best to use the 
system which is currently used by most users.

Christian


>>
>> But as you said below backward-compatibility is always lost, so the
>> question which system to use to build R/BioC is always tricky. Maybe,
>> the best (?) decision would be to use the system which most Mac users
>> are currently using, but I don't know.
>>
>> Best regards,
>> Christian
>>
>>>>
>>>> However, Sierra is different, and when the CRAN people are
>>>> experimenting
>>>> with clang 4.0.0 for producing the Mac binaries, as Herve has
>>>> mentioned,
>>>> then backwards-compatibility would probably be lost anyhow.
>>>
>>> I think you misunderstood what Dan said. Backward-compatibility is
>>> always lost i.e. binaries built on a given OS X versions are not
>>> guaranteed to be backward compatible with older OS X versions. That's
>>> why building them on the latest OS X version is a bad idea.
>>>
>>>>
>>>> But I understand that this is a decision the CRAN people have to make.
>>>
>>> You're welcome to discuss this choice on the R-SIG-Mac mailing list.
>>>
>>> Cheers,
>>> H.
>>>
>>>>
>>>> Best regards,
>>>> Christian
>>>>
>>>>
>>>> On 03/24/17 01:10, Dan Tenenbaum wrote:
>>>>>
>>>>>
>>>>> ----- Original Message -----
>>>>>> From: "Hervé Pagès" <hpages at fredhutch.org>
>>>>>> To: "cstrato" <cstrato at aon.at>, "bioc-devel"
>>>>>> <bioc-devel at r-project.org>
>>>>>> Sent: Thursday, March 23, 2017 12:14:38 PM
>>>>>> Subject: Re: [Bioc-devel] xps build problem on veracruz2
>>>>>
>>>>>> On 03/23/2017 11:09 AM, cstrato wrote:
>>>>>>> Dear Herve,
>>>>>>>
>>>>>>> Thank you for your explanation.
>>>>>>>
>>>>>>> The reason that xps does not work with ROOT 6 is that I have
>>>>>>> tried it
>>>>>>> but there seem to be so many changes, that I did not succeed.
>>>>>>> Since for xps there is no advantage using ROOT 6 vs ROOT 5, and
>>>>>>> ROOT 5
>>>>>>> was still supported, I have decided to stay with ROOT 5.
>>>>>>
>>>>>> OK
>>>>>>
>>>>>>>
>>>>>>> BTW, I have also one question:
>>>>>>> Why did you decide to set up a new Mac with El Capitan instead of
>>>>>>> using
>>>>>>> the newest OS Sierra? (I have the impression that most Mac users are
>>>>>>> either happy to stay with their old OS or they upgrade to the newest
>>>>>>> one.)
>>>>>>
>>>>>> Same reason as for the choice of compilers: that's what the R folks
>>>>>> decided to use for producing the Mac binaries of R and CRAN packages.
>>>>>> We're just following their lead on that.
>>>>>>
>>>>>
>>>>> Also, it's always good not to require users to upgrade if they don't
>>>>> have to. Building on El Capitan means users will not have to upgrade
>>>>> to macOS Sierra if they don't want to. Building on Sierra would mean R
>>>>> and packages would not be backwards-compatible with El Capitan.
>>>>>
>>>>> But it's a tradeoff that also involves the difficulty of maintaining
>>>>> build machines with old OSes, and wanting to take advantage of newer
>>>>> compiler technology. Otherwise R/Bioc would still be building on
>>>>> Mavericks, or Snow Leopard...
>>>>>
>>>>> Dan
>>>>>
>>>>>
>>>>>> Cheers,
>>>>>> H.
>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Christian
>>>>>>>
>>>>>>>
>>>>>>> On 03/23/17 17:47, Hervé Pagès wrote:
>>>>>>>> Hi Christian,
>>>>>>>>
>>>>>>>> The CRAN folks are currently experimenting with clang 4.0.0 for
>>>>>>>> producing the Mac binaries of R and CRAN packages so we are using
>>>>>>>> the same on veracruz2. This is a version of clang that is ahead of
>>>>>>>> what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
>>>>>>>> to compile ROOT from source on veracruz2.
>>>>>>>>
>>>>>>>> BTW any reason not to make xps work with ROOT 6?
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> H.
>>>>>>>>
>>>>>>>> On 03/23/2017 07:28 AM, cstrato wrote:
>>>>>>>>> Dear Valerie,
>>>>>>>>>
>>>>>>>>> I have seen that you have set up a new Mac server, veracruz2,
>>>>>>>>> running El
>>>>>>>>> Capitan.
>>>>>>>>>
>>>>>>>>> Although the development version of xps does even run on Mac OS
>>>>>>>>> Sierra,
>>>>>>>>> one issue still remains the same:
>>>>>>>>>
>>>>>>>>> You need to install the latest ROOT version 5, since xps does not
>>>>>>>>> run
>>>>>>>>> with ROOT 6!
>>>>>>>>>
>>>>>>>>> So you need to install on veracruz2 the same root version that you
>>>>>>>>> have
>>>>>>>>> installed on toluca2 running Maverics, i.e.
>>>>>>>>> root_v5.34.36.macosx64-10.11-clang70.dmg
>>>>>>>>>
>>>>>>>>> However, if you have installed on El Capitan XCode 8.x instead of
>>>>>>>>> XCode
>>>>>>>>> 7.x, then you need to compile ROOT from source, i.e.:
>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e=
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The README file of xps does explain how to compile ROOT for
>>>>>>>>> Sierra. This
>>>>>>>>> should also be valid for El Capitan running XCode 8.x.
>>>>>>>>>
>>>>>>>>> Thank you in advance.
>>>>>>>>> Best regards,
>>>>>>>>> Christian
>>>>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>>>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>>>>>>>>> V.i.e.n.n.a           A.u.s.t.r.i.a
>>>>>>>>> e.m.a.i.l:        cstrato at aon.at
>>>>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&e=
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Hervé Pagès
>>>>>>
>>>>>> Program in Computational Biology
>>>>>> Division of Public Health Sciences
>>>>>> Fred Hutchinson Cancer Research Center
>>>>>> 1100 Fairview Ave. N, M1-B514
>>>>>> P.O. Box 19024
>>>>>> Seattle, WA 98109-1024
>>>>>>
>>>>>> E-mail: hpages at fredhutch.org
>>>>>> Phone:  (206) 667-5791
>>>>>> Fax:    (206) 667-1319
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e=
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>
>

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